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Topokaryotyping demonstrates single cell variability and stress dependent variations in nuclear envelope associated domains

Analysis of large-scale interphase genome positioning with reference to a nuclear landmark has recently been studied using sequencing-based single cell approaches. However, these approaches are dependent upon technically challenging, time consuming and costly high throughput sequencing technologies,...

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Autores principales: Jurisic, Anamarija, Robin, Chloé, Tarlykov, Pavel, Siggens, Lee, Schoell, Brigitte, Jauch, Anna, Ekwall, Karl, Sørensen, Claus Storgaard, Lipinski, Marc, Shoaib, Muhammad, Ogryzko, Vasily
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6294560/
https://www.ncbi.nlm.nih.gov/pubmed/30215776
http://dx.doi.org/10.1093/nar/gky818
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author Jurisic, Anamarija
Robin, Chloé
Tarlykov, Pavel
Siggens, Lee
Schoell, Brigitte
Jauch, Anna
Ekwall, Karl
Sørensen, Claus Storgaard
Lipinski, Marc
Shoaib, Muhammad
Ogryzko, Vasily
author_facet Jurisic, Anamarija
Robin, Chloé
Tarlykov, Pavel
Siggens, Lee
Schoell, Brigitte
Jauch, Anna
Ekwall, Karl
Sørensen, Claus Storgaard
Lipinski, Marc
Shoaib, Muhammad
Ogryzko, Vasily
author_sort Jurisic, Anamarija
collection PubMed
description Analysis of large-scale interphase genome positioning with reference to a nuclear landmark has recently been studied using sequencing-based single cell approaches. However, these approaches are dependent upon technically challenging, time consuming and costly high throughput sequencing technologies, requiring specialized bioinformatics tools and expertise. Here, we propose a novel, affordable and robust microscopy-based single cell approach, termed Topokaryotyping, to analyze and reconstruct the interphase positioning of genomic loci relative to a given nuclear landmark, detectable as banding pattern on mitotic chromosomes. This is accomplished by proximity-dependent histone labeling, where biotin ligase BirA fused to nuclear envelope marker Emerin was coexpressed together with Biotin Acceptor Peptide (BAP)-histone fusion followed by (i) biotin labeling, (ii) generation of mitotic spreads, (iii) detection of the biotin label on mitotic chromosomes and (iv) their identification by karyotyping. Using Topokaryotyping, we identified both cooperativity and stochasticity in the positioning of emerin-associated chromatin domains in individual cells. Furthermore, the chromosome-banding pattern showed dynamic changes in emerin-associated domains upon physical and radiological stress. In summary, Topokaryotyping is a sensitive and reliable technique to quantitatively analyze spatial positioning of genomic regions interacting with a given nuclear landmark at the single cell level in various experimental conditions.
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spelling pubmed-62945602018-12-21 Topokaryotyping demonstrates single cell variability and stress dependent variations in nuclear envelope associated domains Jurisic, Anamarija Robin, Chloé Tarlykov, Pavel Siggens, Lee Schoell, Brigitte Jauch, Anna Ekwall, Karl Sørensen, Claus Storgaard Lipinski, Marc Shoaib, Muhammad Ogryzko, Vasily Nucleic Acids Res Methods Online Analysis of large-scale interphase genome positioning with reference to a nuclear landmark has recently been studied using sequencing-based single cell approaches. However, these approaches are dependent upon technically challenging, time consuming and costly high throughput sequencing technologies, requiring specialized bioinformatics tools and expertise. Here, we propose a novel, affordable and robust microscopy-based single cell approach, termed Topokaryotyping, to analyze and reconstruct the interphase positioning of genomic loci relative to a given nuclear landmark, detectable as banding pattern on mitotic chromosomes. This is accomplished by proximity-dependent histone labeling, where biotin ligase BirA fused to nuclear envelope marker Emerin was coexpressed together with Biotin Acceptor Peptide (BAP)-histone fusion followed by (i) biotin labeling, (ii) generation of mitotic spreads, (iii) detection of the biotin label on mitotic chromosomes and (iv) their identification by karyotyping. Using Topokaryotyping, we identified both cooperativity and stochasticity in the positioning of emerin-associated chromatin domains in individual cells. Furthermore, the chromosome-banding pattern showed dynamic changes in emerin-associated domains upon physical and radiological stress. In summary, Topokaryotyping is a sensitive and reliable technique to quantitatively analyze spatial positioning of genomic regions interacting with a given nuclear landmark at the single cell level in various experimental conditions. Oxford University Press 2018-12-14 2018-09-12 /pmc/articles/PMC6294560/ /pubmed/30215776 http://dx.doi.org/10.1093/nar/gky818 Text en © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Methods Online
Jurisic, Anamarija
Robin, Chloé
Tarlykov, Pavel
Siggens, Lee
Schoell, Brigitte
Jauch, Anna
Ekwall, Karl
Sørensen, Claus Storgaard
Lipinski, Marc
Shoaib, Muhammad
Ogryzko, Vasily
Topokaryotyping demonstrates single cell variability and stress dependent variations in nuclear envelope associated domains
title Topokaryotyping demonstrates single cell variability and stress dependent variations in nuclear envelope associated domains
title_full Topokaryotyping demonstrates single cell variability and stress dependent variations in nuclear envelope associated domains
title_fullStr Topokaryotyping demonstrates single cell variability and stress dependent variations in nuclear envelope associated domains
title_full_unstemmed Topokaryotyping demonstrates single cell variability and stress dependent variations in nuclear envelope associated domains
title_short Topokaryotyping demonstrates single cell variability and stress dependent variations in nuclear envelope associated domains
title_sort topokaryotyping demonstrates single cell variability and stress dependent variations in nuclear envelope associated domains
topic Methods Online
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6294560/
https://www.ncbi.nlm.nih.gov/pubmed/30215776
http://dx.doi.org/10.1093/nar/gky818
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